Whole-Genome Analysis of Genomic Diversity and Antimicrobial Resistance Among Clinical Klebsiella pneumoniae Isolates from Farwaniya Hospital in Kuwait.
5 affiliations
- 1Serology and Molecular Microbiology Reference Laboratory, Mubarak Al-Kabeer Hospital, Ministry of Health, Kuwait City 13110, Kuwait.
- 2Dasman Diabetes Institute, Kuwait City 15462, Kuwait.
- 3Department of Microbiology, College of Medicine, Kuwait University, Kuwait City 13110, Kuwait.
- 4Innomedics Medical Company, Kuwait City 13114, Kuwait.
- 5Microbiology Unit, Department of Laboratory Medicine, Farwaniya Hospital, Ministry of Health, Kuwait City 81004, Kuwait.
Abstract
Background:K. pneumoniae is a major opportunistic pathogen recognized by the World Health Organization as a critical-priority antimicrobial-resistant pathogen. This study characterized isolates for antibiotic resistance determinants, virulence-associated genes, mobile genetic elements, and population structure of the isolates, and evaluated the correlation between antimicrobial resistance genotype and phenotype. Methods: Ninety-five isolates were collected from different clinical specimens in August-December 2024 in Farwaniya Hospital, Kuwait. Fifty-six isolates were selected for whole-genome sequencing (WGS) using Oxford Nanopore Technology. Antimicrobial resistance genes, virulence-associated genes, plasmid replicons, insertion sequences, transposons, and sequence types were identified using different bioinformatics tools. Results: The 56 isolates comprised 47 multidrug-resistant and 9 non-multidrug-resistant isolates. β-lactam resistance genes were detected in all isolates, with blaSHV (96.4%), blaCTX-M-15 (75.0%), blaOXA (64.3%), and blaNDM-5 (30.4%) being the most prevalent. IncFIB(K) was the predominant plasmid replicon, whereas ISSen9, IS26, and IS903 were the most common insertion sequences. Twenty-eight virulence-associated genes were identified, with enterobactin-associated genes, fimbrial adhesion genes, and ompA detected in over 90% of the isolates. MLST identified 32 sequence types, including eight novel sequence types, with ST16 and ST147 predominating. High genotype-phenotype concordance was observed for cephalosporins (87.5%) and penicillins (85.7%). Conclusions:K. pneumoniae isolates exhibited extensive genomic diversity and multidrug resistance associated with multiple resistance determinants, mobile genetic elements, and high-risk lineages. These findings highlight the value of WGS for antimicrobial resistance surveillance and support continued genomic monitoring to support infection prevention and antimicrobial stewardship programs in Kuwait.
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BibTeX
@article{alatar2026wholegenome,
title = {{Whole-Genome Analysis of Genomic Diversity and Antimicrobial Resistance Among Clinical Klebsiella pneumoniae Isolates from Farwaniya Hospital in Kuwait.}},
author = {Fatemah Alatar and Samar S Boswihi and Hussain A Safar and Anfal Al-Adwani and Abu Salim Mustafa and Wadha Alfouzan},
journal = {Antibiotics (Basel, Switzerland)},
year = {2026},
month = sep,
doi = {10.3390/antibiotics15100960},
url = {https://europepmc.org/article/MED/42938701},
note = {CC BY},
}
RIS
TY - JOUR
TI - Whole-Genome Analysis of Genomic Diversity and Antimicrobial Resistance Among Clinical Klebsiella pneumoniae Isolates from Farwaniya Hospital in Kuwait.
AU - Fatemah Alatar
AU - Samar S Boswihi
AU - Hussain A Safar
AU - Anfal Al-Adwani
AU - Abu Salim Mustafa
AU - Wadha Alfouzan
PY - 2026
DA - 2026/09/28
JO - Antibiotics (Basel, Switzerland)
DO - 10.3390/antibiotics15100960
UR - https://europepmc.org/article/MED/42938701
AB - Background:K. pneumoniae is a major opportunistic pathogen recognized by the World Health Organization as a critical-priority antimicrobial-resistant pathogen. This study characterized isolates for antibiotic resistance determinants, virulence-associated genes, mobile genetic elements, and population structure of the isolates, and evaluated the correlation between antimicrobial resistance genotype and phenotype. Methods: Ninety-five isolates were collected from different clinical specimens in August-December 2024 in Farwaniya Hospital, Kuwait. Fifty-six isolates were selected for whole-genome sequencing (WGS) using Oxford Nanopore Technology. Antimicrobial resistance genes, virulence-associated genes, plasmid replicons, insertion sequences, transposons, and sequence types were identified using different bioinformatics tools. Results: The 56 isolates comprised 47 multidrug-resistant and 9 non-multidrug-resistant isolates. β-lactam resistance genes were detected in all isolates, with blaSHV (96.4%), blaCTX-M-15 (75.0%), blaOXA (64.3%), and blaNDM-5 (30.4%) being the most prevalent. IncFIB(K) was the predominant plasmid replicon, whereas ISSen9, IS26, and IS903 were the most common insertion sequences. Twenty-eight virulence-associated genes were identified, with enterobactin-associated genes, fimbrial adhesion genes, and ompA detected in over 90% of the isolates. MLST identified 32 sequence types, including eight novel sequence types, with ST16 and ST147 predominating. High genotype-phenotype concordance was observed for cephalosporins (87.5%) and penicillins (85.7%). Conclusions:K. pneumoniae isolates exhibited extensive genomic diversity and multidrug resistance associated with multiple resistance determinants, mobile genetic elements, and high-risk lineages. These findings highlight the value of WGS for antimicrobial resistance surveillance and support continued genomic monitoring to support infection prevention and antimicrobial stewardship programs in Kuwait.
SN - 2079-6382
ER -